/usr/lib/R/site-library/BiocGenerics/unitTests/test_updateObject.R is in r-bioc-biocgenerics 0.8.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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test_updateObject_list <- function()
{
setClass("A",
representation(x="numeric"), prototype(x=1:10),
where=.GlobalEnv)
a <- new("A")
l <- list(a,a)
checkTrue(identical(l, updateObject(l)))
setMethod("updateObject", "A",
function(object, ..., verbose=FALSE) {
if (verbose) message("updateObject object = 'A'")
object@x <- -object@x
object
},
where=.GlobalEnv)
obj <- updateObject(l)
checkTrue(identical(lapply(l, function(elt) { elt@x <- -elt@x; elt }),
obj))
removeMethod("updateObject", "A", where=.GlobalEnv)
removeClass("A", where=.GlobalEnv)
}
test_updateObject_env <- function()
{
opts <- options()
options(warn=-1)
e <- new.env()
e$x=1
e$.x=1
obj <- updateObject(e)
checkTrue(identical(e,obj)) # modifies environment
lockEnvironment(e)
obj <- updateObject(e) # copies environment
checkTrue(identical(lapply(ls(e, all=TRUE), function(x) x),
lapply(ls(obj, all=TRUE), function(x) x)))
checkTrue(!identical(e, obj)) # different environments
e <- new.env()
e$x=1
e$.x=1
lockBinding("x", e)
checkException(updateObject(e), silent=TRUE)
lockEnvironment(e)
obj <- updateObject(e)
checkTrue(TRUE==bindingIsLocked("x", obj)) # R bug, 14 May, 2006, fixed
checkTrue(FALSE==bindingIsLocked(".x", obj))
options(opts)
}
test_updateObject_defaults <- function()
{
x <- 1:10
checkTrue(identical(x, updateObject(x)))
}
test_updateObject_S4 <- function()
{
setClass("A",
representation=representation(
x="numeric"),
prototype=list(x=1:5),
where=.GlobalEnv)
.__a__ <- new("A")
setClass("A",
representation=representation(
x="numeric",
y="character"),
where=.GlobalEnv)
checkException(validObject(.__a__), silent=TRUE) # now out-of-date
.__a__@x <- 1:5
a <- updateObject(.__a__)
checkTrue(validObject(a))
checkIdentical(1:5, a@x)
removeClass("A", where=.GlobalEnv)
}
test_updateObject_setClass <- function()
{
setClass("A",
representation(x="numeric"),
prototype=prototype(x=1:10),
where=.GlobalEnv)
a <- new("A")
checkTrue(identical(a,updateObject(a)))
removeClass("A", where=.GlobalEnv)
}
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